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Volume 73, Issue 1

sp. nov., a marine bacterium isolated from coastal seawater No Access

Abstract

A Gram–straining–negative, facultatively anaerobic, motile by means of a polar flagellum and rod-shaped marine bacterium, designated S4M6, was isolated from surface seawater collected in Dongshan Bay (Fujian, PR China). Phylogenetic analysis based on 16S rRNA genes, phylogenomic analysis of single-copy gene families and whole genome data indicated that S4M6 represented a member of the genus . The closest phylogenetic relatives of S4M6 were CGMCC 1.8994 (97.8 % 16S rRNA gene sequence pairwise similarity), LMG 25438 (96.9 %), SZDIS-1 (96.2 %) and M22 (96.1 %). The growth of S4M6 occurred at 15–35 °C (optimum 28 °C), pH 4.0–9.0 (optimum 5.0–7.0) and in the presence of 2–5 % (w/v) NaCl (optimum 3 %). The predominant fatty acids (>10 %) are C, summed feature 3 (Cω7 and/or C  ω6c) and summed feature 8 (Cω7 and/or C  ω6). The DNA G+C content of the assembled genomic sequences was 43.4 % for S4M6. Average nucleotide identity (ANI) values between S4M6 and the reference species were lower than the threshold for species delineation (95–96 %); DNA–DNA hybridization further indicated that S4M6 had less than 70 % similarity to its relatives. On the basis of the polyphasic evidence, strain S4M6 is proposed to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is S4M6 (= KCTC 92312= MCCC 1K06167).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Dongshan Bay , surface seawater and Vibrio sinus sp. nov
Funding
This study was supported by the:
  • Key Technologies Research and Development Program (Award 2021YFC3100503)
    • Principle Award Recipient: WentaoNiu
  • Marine S&T Fund of Fujian Province (Award 2021J05094)
    • Principle Award Recipient: XiaoleiWang
  • National Natural Science Foundation of China (Award 42006085)
    • Principle Award Recipient: XiaoleiWang
© 2023 The Authors
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2023-01-18
2024-05-14
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References

  1. Jiang C, Tanaka M, Nishikawa S, Mino S, Romalde JL et al. Vibrio Clade 3.0: new Vibrionaceae evolutionary units using genome-based approach. Curr Microbiol 2021; 79:1–15 [View Article]
     [Google Scholar]
  2. Zhang X, Lin H, Wang X, Austin B. Significance of Vibrio species in the marine organic carbon cycle—a review. Sci China Earth Sci 2018; 61:1357–1368 [View Article]
     [Google Scholar]
  3. Gomez-Gil B, Tron-Mayén L, Roque A, Turnbull JF, Inglis V et al. Species of Vibrio isolated from hepatopancreas, haemolymph and digestive tract of a population of healthy juvenile Penaeus vannamei. Aquaculture 1998; 163:1–9 [View Article]
     [Google Scholar]
  4. Poli A, Romano I, Mastascusa V, Buono L, Orlando P et al. Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy. Antonie Van Leeuwenhoek 2018; 111:1105–1115 [View Article] [PubMed]
     [Google Scholar]
  5. Huq A, Small EB, West PA, Huq MI, Rahman R et al. Ecological relationships between Vibrio cholerae and planktonic crustacean copepods. Appl Environ Microbiol 1983; 45:275–283 [View Article]
     [Google Scholar]
  6. Wang X, Liu J, Li B, Liang J, Sun H et al. Spatial heterogeneity of Vibrio spp. in sediments of Chinese marginal seas. Appl Environ Microbiol 2019; 85:e03064-18 [View Article]
     [Google Scholar]
  7. Li B, Li Y, Liu R, Xue C, Zhu X et al. Vibrio ouci sp. nov. and Vibrio aquaticus sp. nov., two marine bacteria isolated from the East China Sea. Int J Syst Evol Microbiol 2020; 70:172–179 [View Article]
     [Google Scholar]
  8. Farmer JJ, Michael JJ. Genus I. Vibrio Pacini 1854, 411AL. In Garrity GM. eds Bergey’s Manual of Systematic BacteriologyThe Proteobacteria, Part B, 2nd ed. vol 2 New York: Springer Press; 2005 pp 494–546
     [Google Scholar]
  9. Wang X, Liu J, Liang J, Sun H, Zhang X-H. Spatiotemporal dynamics of the total and active Vibrio spp. populations throughout the Changjiang estuary in China. Environ Microbiol 2020; 22:4438–4455 [View Article] [PubMed]
     [Google Scholar]
  10. Moore ERB, Arnscheidt A, Krüger A, Strömpl C, Mau M et al. Simplified protocols for the preparation of genomic DNA from bacterial cultures. In Molecular Microbial Ecology Manual 1999; 1:1–15
     [Google Scholar]
  11. Zhang Z, Yu T, Xu T, Zhang X-H. Aquimarina pacifica sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:1991–1997 [View Article] [PubMed]
     [Google Scholar]
  12. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  13. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  14. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
     [Google Scholar]
  15. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  16. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
     [Google Scholar]
  17. Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 2010; 11:431 [View Article] [PubMed]
     [Google Scholar]
  18. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2016; 44:D279–D285 [View Article] [PubMed]
     [Google Scholar]
  19. Wang H, Liu J, Wang Y, Zhang X-H. Vibrio marisflavi sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2011; 61:568–573 [View Article] [PubMed]
     [Google Scholar]
  20. Chimetto LA, Cleenwerck I, Moreira APB, Brocchi M, Willems A et al. Vibrio variabilis sp. nov. and Vibrio maritimus sp. nov., isolated from Palythoa caribaeorum. Int J Syst Evol Microbiol 2011; 61:3009–3015 [View Article] [PubMed]
     [Google Scholar]
  21. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article]
     [Google Scholar]
  22. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  23. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article]
     [Google Scholar]
  24. Katoh K, Standley SDM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  25. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article]
     [Google Scholar]
  26. Lin H, Yu M, Wang X, Zhang X-H. Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios. BMC Genomics 2018; 19:135 [View Article] [PubMed]
     [Google Scholar]
  27. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article]
     [Google Scholar]
  28. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article]
     [Google Scholar]
  29. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article]
     [Google Scholar]
  30. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article] [PubMed]
     [Google Scholar]
  31. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article]
     [Google Scholar]
  32. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  33. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article] [PubMed]
     [Google Scholar]
  34. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology, Third Edition. American Society of Microbiology; 2007 pp 19–33
     [Google Scholar]
  35. Tindall BJ, Sikorski J, Smibert RM, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, TM S. eds Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 330–393
     [Google Scholar]
  36. Yoon J-H, Lee K-C, Kho YH, Kang KH, Kim C-J et al. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2002; 52:123–130 [View Article]
     [Google Scholar]
  37. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 1990; 20:1–6
     [Google Scholar]
  38. Meng Y-C, Liu H-C, Zhou Y-G, Cai M, Kang Y. Vibrio gangliei sp. nov., a novel member of Vibrionaceae isolated from sawdust in a pigpen. Int J Syst Evol Microbiol 2018; 68:1969–1974 [View Article] [PubMed]
     [Google Scholar]
  39. Lucena T, Ruvira MA, Arahal DR, Macián MC, Pujalte MJ. Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively. Syst Appl Microbiol 2012; 35:427–431 [View Article]
     [Google Scholar]
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Vibrio sinus sp. nov., a marine bacterium isolated from coastal seawater
Int J Syst Evol Microbiol 73, 005676 (2023); https://doi.org/10.1099/ijsem.0.005676
/content/journal/ijsem/10.1099/ijsem.0.005676
/content/journal/ijsem/10.1099/ijsem.0.005676
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